Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Romain Francois [ctb, cph] ,
Francesc Alted [ctb, cph] ,
Bryce Chamberlain [ctb] ,
Sal [...truncated...]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.25.7 dated 2023-12-06 and 0.26.1 dated 2024-03-08
ChangeLog | 4 DESCRIPTION | 10 - MD5 | 37 +++--- NAMESPACE | 3 R/RcppExports.R | 12 ++ R/zz_help_files.R | 50 ++++++++ build/vignette.rds |binary configure | 2 configure.ac | 2 data/starnames.rda |binary inst/extra_tests/benchmark_testing_between_versions.R | 1 inst/extra_tests/regression_testing.R | 2 inst/extra_tests/revdep_check.R | 2 inst/include/qs_RcppExports.h | 58 +++++++++ man/get_altrep_class_info.Rd |only man/register_altrep_class.Rd |only man/unregister_altrep_class.Rd |only src/RcppExports.cpp | 108 ++++++++++++++++++ src/qs_common.h | 14 +- src/qs_functions.cpp | 37 ++++++ src/qs_serialize_common.h | 101 +++++++++------- 21 files changed, 363 insertions(+), 80 deletions(-)
Title: Predicted Risk for CVD using Pooled Cohort Equations, PREVENT
Equations, and Other Contemporary CVD Risk Calculators
Description: The 2017 American College of Cardiology and American Heart
Association blood pressure guideline recommends using 10-year predicted
atherosclerotic cardiovascular disease risk to guide the decision to
initiate or intensify antihypertensive medication. The guideline recommends
using the Pooled Cohort risk prediction equations to predict 10-year
atherosclerotic cardiovascular disease risk. This package implements the
original Pooled Cohort risk prediction equations and also incorporates
updated versions based on more contemporary data and statistical methods.
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>
Diff between PooledCohort versions 0.0.1 dated 2021-04-19 and 0.0.2 dated 2024-03-08
PooledCohort-0.0.1/PooledCohort/R/predict_ascvd_risk.R |only PooledCohort-0.0.2/PooledCohort/DESCRIPTION | 25 PooledCohort-0.0.2/PooledCohort/LICENSE | 4 PooledCohort-0.0.2/PooledCohort/MD5 | 26 PooledCohort-0.0.2/PooledCohort/NAMESPACE | 10 PooledCohort-0.0.2/PooledCohort/R/pcr.R |only PooledCohort-0.0.2/PooledCohort/R/predict_risk.R |only PooledCohort-0.0.2/PooledCohort/R/prevent.R |only PooledCohort-0.0.2/PooledCohort/R/sysdata.rda |only PooledCohort-0.0.2/PooledCohort/README.md | 97 PooledCohort-0.0.2/PooledCohort/man/predict_10yr_ascvd_risk.Rd | 773 +++- PooledCohort-0.0.2/PooledCohort/tests/testthat.R | 8 PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_10yr_ascvd_risk.R |only PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_10yr_chd_risk.R |only PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_10yr_cvd_risk.R |only PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_10yr_hf_risk.R |only PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_10yr_stroke_risk.R |only PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_30yr_ascvd_risk.R |only PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_ascvd_risk.R | 1735 +++++----- PooledCohort-0.0.2/PooledCohort/tests/testthat/test-predict_cvd_risk.R |only 20 files changed, 1652 insertions(+), 1026 deletions(-)
Title: Simple Tools to Compute Landscape Connectivity Metrics
Description: Provides functions to upload vectorial data and derive landscape
connectivity metrics in habitat or matrix systems. Additionally, includes an
approach to assess individual patch contribution to the overall landscape
connectivity, enabling the prioritization of habitat patches. The computation
of landscape connectivity and patch importance are very useful in Landscape
Ecology research. The metrics available are: number of components, number of
links, size of the largest component, mean size of components, class coincidence
probability, landscape coincidence probability, characteristic path length,
expected cluster size, area-weighted flux and integral index of connectivity.
Pascual-Hortal, L., and Saura, S. (2006) <doi:10.1007/s10980-006-0013-z>
Urban, D., and Keitt, T. (2001) <doi:10.2307/2679983>
Laita, A., Kotiaho, J., Monkkonen, M. (2011) <doi:10.1007/s10980-011-9620-4>.
Author: Frederico Mestre [aut, cre],
Bruno Silva [aut],
Benjamin Branoff [ctb]
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between lconnect versions 0.1.1 dated 2021-02-06 and 0.1.2 dated 2024-03-08
DESCRIPTION | 20 +++++++++++--------- MD5 | 23 +++++++++++++---------- NAMESPACE | 4 +++- R/RcppExports.R |only R/con_metric.R | 15 ++++++--------- R/patch_imp.R | 10 +++++----- R/plot.lconnect.R | 13 +++++++++++-- R/plot.pimp.R | 2 +- R/remove_patch.R | 14 +++++++++++--- R/upload_land.R | 4 ++-- man/con_metric.Rd | 2 ++ man/patch_imp.Rd | 2 +- src |only 13 files changed, 66 insertions(+), 43 deletions(-)
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer and in
Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009).
Functional Data Analysis with R and Matlab (Springer).
The package includes data sets and script files working many examples
including all but one of the 76 figures in this latter book. Matlab versions
are available by ftp from
<https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: James Ramsay [aut, cre],
Giles Hooker [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <ramsay@psych.mcgill.ca>
Diff between fda versions 6.1.7 dated 2024-03-01 and 6.1.8 dated 2024-03-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/smooth.basis1.R | 4 ++-- inst/doc/BasisBasics.html | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut],
Andrea Paz [aut],
Bethany A. Johnson [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [aut, cre],
Robert P. Anderson [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
Diff between wallace versions 2.1.1 dated 2023-12-07 and 2.1.2 dated 2024-03-08
wallace-2.1.1/wallace/inst/shiny/www/img/hannahO.png |only wallace-2.1.1/wallace/inst/shiny/www/img/valentina.png |only wallace-2.1.2/wallace/DESCRIPTION | 14 ++--- wallace-2.1.2/wallace/MD5 | 31 +++++------ wallace-2.1.2/wallace/NEWS.md | 8 ++ wallace-2.1.2/wallace/R/helper_functions.R | 3 - wallace-2.1.2/wallace/R/xfer_time.R | 3 - wallace-2.1.2/wallace/README.md | 4 - wallace-2.1.2/wallace/inst/shiny/Rmd/text_about.Rmd | 2 wallace-2.1.2/wallace/inst/shiny/Rmd/text_intro_tab.Rmd | 2 wallace-2.1.2/wallace/inst/shiny/Rmd/text_team.Rmd | 10 ++- wallace-2.1.2/wallace/inst/shiny/Rmd/userReport_intro.Rmd | 2 wallace-2.1.2/wallace/inst/shiny/modules/occs_queryDb.yml | 2 wallace-2.1.2/wallace/inst/shiny/modules/xfer_time.R | 39 +++++++++----- wallace-2.1.2/wallace/inst/shiny/www/img/daniel.jpeg |only wallace-2.1.2/wallace/inst/shiny/www/img/hannahO.jpeg |only wallace-2.1.2/wallace/inst/shiny/www/img/valentina.jpeg |only wallace-2.1.2/wallace/man/xfer_time.Rd | 2 wallace-2.1.2/wallace/tests/testthat/test_occs_queryDb.R | 8 +- 19 files changed, 79 insertions(+), 51 deletions(-)
Title: Data Processing of SMN Hi-Res Weather Forecast from 'AWS'
Description: Exploration of Weather Research & Forecasting ('WRF') Model data
of Servicio Meteorologico Nacional (SMN) from Amazon Web Services
(<https://registry.opendata.aws/smn-ar-wrf-dataset/>) cloud. The package
provides the possibility of data downloading, processing and correction
methods. It also has map management and series exploration of available
meteorological variables of 'WRF' forecast.
Author: Gonzalo Diaz [cre, aut]
Maintainer: Gonzalo Diaz <gonzalomartindiaz22@gmail.com>
Diff between aws.wrfsmn versions 0.0.2 dated 2024-03-06 and 0.0.3 dated 2024-03-08
DESCRIPTION | 6 MD5 | 20 NAMESPACE | 1 NEWS.md | 6 R/mg_evaluation.R | 55 R/multiple_guidance.R | 11 inst/doc/Multiple-Linear-Regression-Correction.R | 4 inst/doc/Multiple-Linear-Regression-Correction.Rmd | 10 inst/doc/Multiple-Linear-Regression-Correction.html | 2210 ++++++++++---------- tests/testthat/test-Input_entry.R |only tests/testthat/test-Output.R |only vignettes/Multiple-Linear-Regression-Correction.Rmd | 10 12 files changed, 1175 insertions(+), 1158 deletions(-)
Title: Summarize Data for Scientific Publication
Description: Create and format tables and APA statistics for
scientific publication. This includes making a 'Table 1'
to summarize demographics across groups, correlation tables
with significance indicated by stars, and extracting formatted
statistical summarizes from simple tests for in-text notation.
The package also includes functions for Winsorizing data based
on a Z-statistic cutoff.
Author: David Pagliaccio [aut, cre]
Maintainer: David Pagliaccio <david.pagliaccio@gmail.com>
Diff between scipub versions 1.2.2 dated 2021-03-18 and 1.2.3 dated 2024-03-08
DESCRIPTION | 8 MD5 | 12 - NEWS.md | 4 R/FullTable1.R | 4 R/apastat.R | 8 build/vignette.rds |binary inst/doc/scipub_vignette.html | 483 ++++++++++++++++++++++++------------------ 7 files changed, 302 insertions(+), 217 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.5.0 dated 2023-12-08 and 2.5.1 dated 2024-03-08
mizer-2.5.0/mizer/inst/shiny/selectivity_effects/rsconnect |only mizer-2.5.1/mizer/DESCRIPTION | 11 mizer-2.5.1/mizer/MD5 | 142 +++++----- mizer-2.5.1/mizer/NEWS.md | 10 mizer-2.5.1/mizer/R/MizerSim-class.R | 2 mizer-2.5.1/mizer/R/extension.R | 2 mizer-2.5.1/mizer/R/project.R | 14 mizer-2.5.1/mizer/R/project_methods.R | 3 mizer-2.5.1/mizer/R/rate_functions.R | 8 mizer-2.5.1/mizer/R/setBevertonHolt.R | 2 mizer-2.5.1/mizer/R/setReproduction.R | 5 mizer-2.5.1/mizer/R/steady.R | 4 mizer-2.5.1/mizer/build |only mizer-2.5.1/mizer/inst/WORDLIST | 2 mizer-2.5.1/mizer/inst/doc |only mizer-2.5.1/mizer/man/animateSpectra.Rd | 2 mizer-2.5.1/mizer/man/figures/Beverton-Holt-plot-1.png |binary mizer-2.5.1/mizer/man/getBiomass.Rd | 4 mizer-2.5.1/mizer/man/getDiet.Rd | 4 mizer-2.5.1/mizer/man/getEGrowth.Rd | 4 mizer-2.5.1/mizer/man/getERepro.Rd | 2 mizer-2.5.1/mizer/man/getEReproAndGrowth.Rd | 2 mizer-2.5.1/mizer/man/getESpawning.Rd | 2 mizer-2.5.1/mizer/man/getEncounter.Rd | 4 mizer-2.5.1/mizer/man/getFMort.Rd | 2 mizer-2.5.1/mizer/man/getFMortGear.Rd | 2 mizer-2.5.1/mizer/man/getFeedingLevel.Rd | 4 mizer-2.5.1/mizer/man/getGrowthCurves.Rd | 4 mizer-2.5.1/mizer/man/getM2.Rd | 4 mizer-2.5.1/mizer/man/getM2Background.Rd | 4 mizer-2.5.1/mizer/man/getMort.Rd | 4 mizer-2.5.1/mizer/man/getN.Rd | 4 mizer-2.5.1/mizer/man/getPredMort.Rd | 4 mizer-2.5.1/mizer/man/getPredRate.Rd | 4 mizer-2.5.1/mizer/man/getRDD.Rd | 4 mizer-2.5.1/mizer/man/getRDI.Rd | 4 mizer-2.5.1/mizer/man/getRates.Rd | 4 mizer-2.5.1/mizer/man/getResourceMort.Rd | 4 mizer-2.5.1/mizer/man/getSSB.Rd | 4 mizer-2.5.1/mizer/man/getZ.Rd | 4 mizer-2.5.1/mizer/man/mizerEGrowth.Rd | 4 mizer-2.5.1/mizer/man/mizerERepro.Rd | 2 mizer-2.5.1/mizer/man/mizerEReproAndGrowth.Rd | 2 mizer-2.5.1/mizer/man/mizerEncounter.Rd | 4 mizer-2.5.1/mizer/man/mizerFMort.Rd | 2 mizer-2.5.1/mizer/man/mizerFMortGear.Rd | 2 mizer-2.5.1/mizer/man/mizerFeedingLevel.Rd | 4 mizer-2.5.1/mizer/man/mizerMort.Rd | 4 mizer-2.5.1/mizer/man/mizerPredMort.Rd | 4 mizer-2.5.1/mizer/man/mizerPredRate.Rd | 4 mizer-2.5.1/mizer/man/mizerRDI.Rd | 4 mizer-2.5.1/mizer/man/mizerRates.Rd | 4 mizer-2.5.1/mizer/man/mizerResourceMort.Rd | 4 mizer-2.5.1/mizer/man/plotBiomass.Rd | 2 mizer-2.5.1/mizer/man/plotDiet.Rd | 2 mizer-2.5.1/mizer/man/plotFMort.Rd | 2 mizer-2.5.1/mizer/man/plotFeedingLevel.Rd | 2 mizer-2.5.1/mizer/man/plotGrowthCurves.Rd | 2 mizer-2.5.1/mizer/man/plotM2.Rd | 2 mizer-2.5.1/mizer/man/plotMizerSim.Rd | 4 mizer-2.5.1/mizer/man/plotPredMort.Rd | 2 mizer-2.5.1/mizer/man/plotSpectra.Rd | 2 mizer-2.5.1/mizer/man/plotting_functions.Rd | 4 mizer-2.5.1/mizer/man/projectToSteady.Rd | 2 mizer-2.5.1/mizer/man/steady.Rd | 2 mizer-2.5.1/mizer/tests/testthat/Rplots.pdf |only mizer-2.5.1/mizer/tests/testthat/_snaps/plots/plotpredmort-truncated.new.svg |only mizer-2.5.1/mizer/tests/testthat/_snaps/plots/plotpredmort-truncated.svg | 2 mizer-2.5.1/mizer/tests/testthat/test-extension.R | 2 mizer-2.5.1/mizer/tests/testthat/test-plots.R | 5 mizer-2.5.1/mizer/tests/testthat/test-rate_functions.R | 2 mizer-2.5.1/mizer/tests/testthat/test-setReproduction.R | 2 mizer-2.5.1/mizer/vignettes/mizer.Rmd |only mizer-2.5.1/mizer/vignettes/reflib.bib |only mizer-2.5.1/mizer/vignettes/vignette_images |only 75 files changed, 200 insertions(+), 174 deletions(-)
Title: Core Functionality for Environmental Time Series
Description: Utility functions for working with environmental time series data from known
locations. The compact data model is structured as a list with two dataframes. A
'meta' dataframe contains spatial and measuring device metadata associated with
deployments at known locations. A 'data' dataframe contains a 'datetime' column
followed by columns of measurements associated with each "device-deployment".
Ephemerides calculations are based on code originally found in NOAA's
"Solar Calculator" <https://gml.noaa.gov/grad/solcalc/>.
Author: Jonathan Callahan [aut, cre],
Hans Martin [ctb],
Eli Grosman [ctb],
Roger Bivand [ctb],
Sebastian Luque [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaTimeSeries versions 0.2.16 dated 2024-01-22 and 0.3.0 dated 2024-03-08
DESCRIPTION | 11 ++-- MD5 | 92 ++++++++++++++++++------------------ NEWS.md | 12 ++++ R/MazamaTimeSeries.R | 4 - R/mts_arrange.R | 1 R/mts_collapse.R | 3 - R/mts_filterData.R | 5 - R/mts_filterDate.R | 9 +-- R/mts_filterDatetime.R | 5 + R/mts_filterMeta.R | 9 +-- R/mts_getDistance.R | 2 R/mts_pull.R | 2 R/mts_sample.R | 3 - R/mts_select.R | 6 +- R/mts_selectWhere.R | 3 - R/mts_setTimeAxis.R | 24 +++++++-- R/mts_slice.R | 1 R/mts_summarize.R | 3 - R/mts_trim.R | 3 - R/mts_trimDate.R | 3 - R/sts_filter.R | 1 R/sts_filterDate.R | 3 - R/sts_filterDatetime.R | 3 - R/sts_summarize.R | 5 + R/sts_trimDate.R | 3 - R/timeInfo.R | 8 +-- R/utils-mts.R | 4 - R/utils-sts.R | 4 - inst/doc/Developer_Style_Guide.Rmd | 2 inst/doc/Developer_Style_Guide.html | 4 - inst/doc/MazamaTimeSeries.Rmd | 8 +-- inst/doc/MazamaTimeSeries.html | 13 ++--- man/mts_filterData.Rd | 4 - man/mts_filterDate.Rd | 8 --- man/mts_filterDatetime.Rd | 2 man/mts_filterMeta.Rd | 8 --- man/mts_getDistance.Rd | 2 man/mts_isValid.Rd | 4 - man/mts_pull.Rd | 2 man/mts_sample.Rd | 2 man/mts_select.Rd | 6 +- man/mts_setTimeAxis.Rd | 25 +++++++-- man/requiredMetaNames.Rd | 4 - man/sts_isValid.Rd | 4 - man/timeInfo.Rd | 8 +-- vignettes/Developer_Style_Guide.Rmd | 2 vignettes/MazamaTimeSeries.Rmd | 8 +-- 47 files changed, 194 insertions(+), 154 deletions(-)
More information about MazamaTimeSeries at CRAN
Permanent link
Title: Curved Text in 'ggplot2'
Description: A 'ggplot2' extension that allows text to follow curved paths.
Curved text makes it easier to directly label paths or neatly annotate in
polar co-ordinates.
Author: Allan Cameron [aut, cre],
Teun van den Brand [aut]
Maintainer: Allan Cameron <Allan.Cameron@nhs.scot>
Diff between geomtextpath versions 0.1.1 dated 2022-08-30 and 0.1.2 dated 2024-03-08
DESCRIPTION | 19 - MD5 | 80 +++--- NAMESPACE | 2 R/geom_labelpath.R | 2 R/geom_textpath.R | 2 R/guide_axis_textpath.R |only R/scales.R | 25 - R/text_helpers.R | 4 R/text_params.R | 4 R/utils.R | 46 +-- README.md | 17 - build/vignette.rds |binary inst/doc/aesthetics.R | 2 inst/doc/aesthetics.html | 379 ++++++++++++++--------------- inst/doc/curved_polar.R | 2 inst/doc/curved_polar.html | 296 +++++++++++----------- inst/doc/geomtextpath.R | 2 inst/doc/geomtextpath.html | 223 ++++++++--------- man/GeomTextpath.Rd | 3 man/figures/README-coord_curvedpolar-1.png |binary man/figures/README-curve-1.png |binary man/figures/README-density_demo-1.png |binary man/figures/README-density_vjust-1.png |binary man/figures/README-fancy_polar-1.png |binary man/figures/README-geom_textsf-1.png |binary man/figures/README-richtext-1.png |binary man/figures/README-smooth-1.png |binary man/figures/README-smooth2-1.png |binary man/figures/README-volcano-1.png |binary man/geom_textabline.Rd | 20 - man/geom_textcontour.Rd | 37 +- man/geom_textcurve.Rd | 20 - man/geom_textdensity.Rd | 23 + man/geom_textdensity2d.Rd | 20 - man/geom_textpath.Rd | 20 - man/geom_textsegment.Rd | 20 - man/geom_textsf.Rd | 20 - man/geom_textsmooth.Rd | 20 - man/guide_axis_textpath.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/_snaps/utils.md | 98 +++---- tests/testthat/test-coord_curvedpolar.R | 6 tests/testthat/test-guide_axis_textpath.R |only 43 files changed, 734 insertions(+), 678 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data
exploration, by creating them, manipulating them, and adding color
helpers to highlight important informations (differences from totals,
comparisons between lines or columns, contributions to variance, margins
of error, etc.). All functions are pipe-friendly and render data frames
which can be easily manipulated. In the same time, time-taking operations
are done with 'data.table' to go faster with big dataframes. Tables can
be exported to 'Excel' and in html with formats and colors.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between tabxplor versions 1.1.2 dated 2024-02-08 and 1.1.3 dated 2024-03-08
DESCRIPTION | 8 MD5 | 14 NEWS.md | 7 R/tab_classes.R | 14 R/tab_xl.R | 6 README.md | 2 inst/doc/tabxplor.html | 1450 ++++++++++++++++++++++++------------------------- man/tab_kable.Rd | 7 8 files changed, 776 insertions(+), 732 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 2.2.2 dated 2024-02-14 and 2.2.3 dated 2024-03-08
DESCRIPTION | 8 MD5 | 26 NEWS.md | 3 R/achillesCodeUse.R | 2 R/drugCodes.R | 654 ++++++----- R/getICD10StandardCodes.R | 569 +++++----- R/mockVocabRef.R | 708 ++++++------ R/runSearch.R | 84 - tests/testthat/test-achillesCodeUse.R | 150 +- tests/testthat/test-drugCodes.R | 241 ++-- tests/testthat/test-findOrphanCodes.R | 136 +- tests/testthat/test-getCandidateCodes.R | 3 tests/testthat/test-getICD10StandardCodes.R | 148 +- tests/testthat/test-summariseCodeUse.R | 1544 ++++++++++++++-------------- 14 files changed, 2149 insertions(+), 2127 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Bootstrap Algorithms for Finite Population Inference
Description: Finite Population bootstrap algorithms to estimate the variance
of the Horvitz-Thompson estimator for single-stage sampling.
For a survey of bootstrap methods for finite populations, see Mashreghi et Al. (2016) <doi:10.1214/16-SS113>.
Author: Roberto Sichera [aut, cre]
Maintainer: Roberto Sichera <rob.sichera@gmail.com>
Diff between bootstrapFP versions 0.4.5 dated 2023-09-02 and 0.4.6 dated 2024-03-08
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 31 ++++++++++++++++--------------- R/generalised.R | 4 ++-- R/utils.R | 2 +- man/select_Uc.Rd | 2 +- 6 files changed, 30 insertions(+), 29 deletions(-)
Title: Rank in Network Meta-Analysis
Description: A supportive collection of functions for gathering and plotting treatment ranking metrics after network meta-analysis.
Author: Chiehfeng Chen [aut] ,
Enoch Kang [aut, cre, trl] ,
Wen-Hsuan Hou [aut] ,
Jin-Hua Chen [aut] ,
Yu-Chieh Chuang [aut] ,
Edwin Chan [aut]
Maintainer: Enoch Kang <y.enoch.kang@gmail.com>
Diff between rankinma versions 0.2.0 dated 2024-01-29 and 0.2.1 dated 2024-03-08
rankinma-0.2.0/rankinma/inst/doc/rankinma_vignette.R |only rankinma-0.2.0/rankinma/inst/doc/rankinma_vignette.Rmd |only rankinma-0.2.0/rankinma/inst/doc/rankinma_vignette.html |only rankinma-0.2.0/rankinma/vignettes/rankinma_vignette.Rmd |only rankinma-0.2.1/rankinma/DESCRIPTION | 13 - rankinma-0.2.1/rankinma/MD5 | 34 +-- rankinma-0.2.1/rankinma/NAMESPACE | 1 rankinma-0.2.1/rankinma/NEWS.md | 25 ++ rankinma-0.2.1/rankinma/R/get_metrics.R | 6 rankinma-0.2.1/rankinma/R/plot_beads.R | 93 +++++++++- rankinma-0.2.1/rankinma/R/plot_spie.R | 6 rankinma-0.2.1/rankinma/R/rankinma-package.R | 1 rankinma-0.2.1/rankinma/R/set_metrics.R | 5 rankinma-0.2.1/rankinma/README.md | 8 rankinma-0.2.1/rankinma/build/vignette.rds |binary rankinma-0.2.1/rankinma/inst/doc/An_overview_on_rankinma.R |only rankinma-0.2.1/rankinma/inst/doc/An_overview_on_rankinma.Rmd |only rankinma-0.2.1/rankinma/inst/doc/An_overview_on_rankinma.html |only rankinma-0.2.1/rankinma/man/GetMetrics.Rd | 6 rankinma-0.2.1/rankinma/man/PlotBeads.Rd | 4 rankinma-0.2.1/rankinma/man/SetMetrics.Rd | 5 rankinma-0.2.1/rankinma/vignettes/An_overview_on_rankinma.Rmd |only 22 files changed, 159 insertions(+), 48 deletions(-)
More information about multipleOutcomes at CRAN
Permanent link
Title: Graphs for Correspondence Analysis
Description: Readable, complete and pretty graphs for correspondence analysis made
with 'FactoMineR'. They can be rendered as interactive 'HTML' plots, showing useful
informations at mouse hover. The interest is not mainly visual but statistical:
it helps the reader to keep in mind the data contained in the cross-table or Burt
table while reading the correspondence analysis, thus preventing over-interpretation.
Most graphs are made with 'ggplot2', which means that you can use the + syntax to
manually add as many graphical pieces you want, or change theme elements. 3D
graphs are made with 'plotly'.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between ggfacto versions 0.2.3 dated 2024-01-25 and 0.3.0 dated 2024-03-08
DESCRIPTION | 31 MD5 | 40 NAMESPACE | 10 NEWS.md | 19 R/geometrical_data_analysis.R | 4160 +++++++++++++++++++++++++++++-- R/utils.R | 421 +++ README.md | 2 man/HCPC_tab.Rd |only man/PCA2.Rd |only man/benzecri_mrv.Rd | 5 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/ggi.Rd | 5 man/ggmca.Rd | 88 man/ggmca_3d.Rd |only man/ggmca_initial_dims.Rd |only man/ggmca_with_base_ref.Rd |only man/ggpca_3d.Rd |only man/ggpca_cor_circle.Rd |only man/mean_sd_tab.Rd |only man/pca_interpret.Rd |only man/tabxplor-data.table.Rd |only 26 files changed, 4563 insertions(+), 218 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Small-area estimation.
Author: Thomas Lumley, Peter Gao
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 4.2-1 dated 2023-05-03 and 4.4-1 dated 2024-03-08
survey |only 1 file changed
Title: Umbrella Review Package for R
Description: A comprehensive range of facilities to perform umbrella reviews with stratification of the evidence in R. The package accomplishes this aim by building on three core functions that: (i) automatically perform all required calculations in an umbrella review (including but not limited to meta-analyses), (ii) stratify evidence according to various classification criteria, and (iii) generate a visual representation of the results. Note that if you are not familiar with R, the core features of this package are available from a web browser (<https://www.metaumbrella.org/>).
Author: Corentin J Gosling [aut, cre],
Aleix Solanes [aut],
Paolo Fusar-Poli [aut],
Joaquim Radua [aut]
Maintainer: Corentin J Gosling <cgosling@parisnanterre.fr>
Diff between metaumbrella versions 1.0.10 dated 2024-01-25 and 1.0.11 dated 2024-03-08
DESCRIPTION | 8 MD5 | 28 NEWS.md | 3 R/check_data.R | 32 R/esb_test.R | 753 +++++++++++------------ R/functions_format_dataset.R | 17 R/functions_multilevel.R | 44 - R/functions_other.R | 2 R/umbrella.R | 4 inst/doc/calculations-details.html | 4 inst/doc/conduct-umbrella.html | 52 - inst/doc/format-dataset.html | 32 inst/doc/generate-forest.html | 4 tests/testthat/test-functions_publication_bias.R | 8 tests/testthat/test-umbrella.R | 4 15 files changed, 512 insertions(+), 483 deletions(-)
Title: Self-Normalization(SN) Based Change-Point Estimation for Time
Series
Description: Implementations self-normalization (SN) based algorithms for
change-points estimation in time series data. This comprises nested
local-window algorithms for detecting changes in both univariate and
multivariate time series developed in Zhao, Jiang and Shao (2022)
<doi:10.1111/rssb.12552>.
Author: Shubo Sun [aut],
Zifeng Zhao [aut, cre],
Feiyu Jiang [aut],
Xiaofeng Shao [aut]
Maintainer: Zifeng Zhao <zzhao2@nd.edu>
Diff between SNSeg versions 1.0.1 dated 2024-01-08 and 1.0.2 dated 2024-03-08
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/SNSeg_HD.R | 9 ++++++--- R/plot_summary_print_HD.R | 13 ++++++++----- inst/doc/SNSeg.R | 12 ++++++------ inst/doc/SNSeg.Rmd | 16 ++++++++-------- inst/doc/SNSeg.html | 25 +++++++++++++------------ man/SNSeg_HD.Rd | 7 +++++-- man/plot.SNSeg_HD.Rd | 11 +++++++---- vignettes/SNSeg.Rmd | 16 ++++++++-------- 10 files changed, 73 insertions(+), 60 deletions(-)
Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elemental indexes are first calculated for a collection
of elemental aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collections of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, ISBN:978-1-107-40496-0), von der Lippe (2001,
ISBN:3-8246-0638-0), and the CPI manual (2020, ISBN:978-1-51354-298-0)
for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.6.0 dated 2023-11-18 and 0.7.0 dated 2024-03-08
DESCRIPTION | 12 MD5 | 151 +- NAMESPACE | 10 NEWS.md | 57 + R/aggregate.piar_index.R | 91 + R/aggregation_structure-class.R | 145 -- R/aggregation_structure.R | 33 R/as_aggregation_structure.R | 13 R/as_index.R | 51 R/chain.R | 33 R/coerce-aggregation_structure.R | 23 R/coerce-index.R | 32 R/contrib.R | 36 R/elemental_index.R | 51 R/extract.piar_index.R | 184 ++- R/head.piar_index.R | 18 R/impute_prices.R | 34 R/index-class.R | 120 -- R/is.na.piar_index.R |only R/levels.piar_aggregation_structure.R |only R/levels.piar_index.R |only R/mean.piar_index.R | 86 + R/merge.piar_index.R | 23 R/price_relative.R | 27 R/split.piar_index.R |only R/stack.piar_index.R | 27 R/summary.piar_index.R | 11 R/time.piar_index.R |only R/update.aggregation_structure.R | 19 R/vcov.aggregate_piar_index.R | 12 R/weights.piar_aggregation_structure.R |only README.md | 41 build/vignette.rds |binary inst/CITATION | 2 inst/doc/piar.R | 213 ++-- inst/doc/piar.Rmd | 223 +++- inst/doc/piar.html | 870 +++++++++-------- man/aggregate.piar_index.Rd | 26 man/aggregation_structure.Rd | 20 man/as.data.frame.piar_index.Rd | 18 man/as.matrix.piar_aggregation_structure.Rd | 9 man/as_aggregation_structure.Rd | 3 man/as_index.Rd | 35 man/chain.Rd | 35 man/contrib.Rd | 18 man/elemental_index.Rd | 22 man/head.piar_index.Rd | 20 man/impute_prices.Rd | 6 man/is.na.piar_index.Rd |only man/is_aggregation_structure.Rd | 4 man/levels.piar_aggregation_structure.Rd |only man/levels.piar_index.Rd | 4 man/mean.piar_index.Rd | 37 man/merge.piar_index.Rd | 25 man/piar-package.Rd | 2 man/piar_index.Rd | 2 man/split.piar_index.Rd |only man/stack.piar_index.Rd | 33 man/sub-.piar_index.Rd | 45 man/summary.piar_index.Rd | 9 man/time.piar_index.Rd | 6 man/update.piar_aggregation_structure.Rd | 13 man/vcov.aggregate_piar_index.Rd | 12 man/weights.piar_aggregation_structure.Rd | 23 tests/Examples/piar-Ex.Rout.save | 396 +++---- tests/testthat/test-aggregate.R | 40 tests/testthat/test-aggregation-structure-attributes.R | 29 tests/testthat/test-aggregation_structure.R | 4 tests/testthat/test-as_aggregation_structure.R | 2 tests/testthat/test-as_index.R | 2 tests/testthat/test-chain.R | 10 tests/testthat/test-coerce-aggregation-structure.R | 2 tests/testthat/test-coerce-index.R | 14 tests/testthat/test-contrib.R | 13 tests/testthat/test-elemental_index.R | 2 tests/testthat/test-extract-index.R | 82 + tests/testthat/test-index-attributes.R | 9 tests/testthat/test-is.na.R |only tests/testthat/test-mean.R | 44 tests/testthat/test-split.R |only tests/testthat/test-update.R | 8 vignettes/piar.Rmd | 223 +++- 82 files changed, 2269 insertions(+), 1686 deletions(-)
Title: Functions and Datasets for the Data Science Course at IBAW
Description: A collection of useful functions and datasets for the Data Science
Course at IBAW in Lucerne.
Author: Stefan Lanz
Maintainer: Stefan Lanz <slanz1137@gmail.com>
Diff between ibawds versions 0.5.0 dated 2022-06-17 and 0.6.0 dated 2024-03-08
DESCRIPTION | 20 +-- LICENSE | 2 MD5 | 60 +++++----- R/cran_packages.R | 60 +++------- R/data.R | 33 +++-- R/dist_plots.R | 14 +- R/grading_tables.R | 15 +- R/voronoi.R | 15 +- README.md | 16 +- build/partial.rdb |binary data/cran_history.rda |binary man/breast_cancer.Rd | 2 man/cran_history.Rd | 25 ++-- man/galton_sons.Rd | 4 man/grading_tables.Rd | 4 man/n_available_packages.Rd | 28 +--- man/wine_quality.Rd | 2 tests/testthat/_snaps/dist_plots/density-plot-binomial.svg | 26 ++-- tests/testthat/_snaps/dist_plots/density-plot-chi2.svg | 6 - tests/testthat/_snaps/dist_plots/density-plot-normal.svg | 6 - tests/testthat/_snaps/dist_plots/density-plot-poisson.svg | 24 ++-- tests/testthat/_snaps/dist_plots/density-plot-weibull.svg | 6 - tests/testthat/_snaps/dist_plots/distribution-plot-binomial.svg | 24 ++-- tests/testthat/_snaps/voronoi/voronoi-default.svg | 6 - tests/testthat/_snaps/voronoi/voronoi-suppress-data.svg | 6 - tests/testthat/_snaps/voronoi/voronoi-uncoloured-data.svg | 6 - tests/testthat/_snaps/voronoi/voronoi-with-data.svg | 6 - tests/testthat/_snaps/voronoi/voronoi-with-options.svg | 6 - tests/testthat/test-cran_packages.R | 29 ++-- tests/testthat/test-grading_tables.R | 8 - tests/testthat/test-install.R | 8 - 31 files changed, 228 insertions(+), 239 deletions(-)
Title: Handwriting Analysis in R
Description: Perform statistical writership analysis of scanned handwritten documents.
Webpage provided at: <https://github.com/CSAFE-ISU/handwriter>.
Author: Iowa State University of Science and Technology on behalf of its Center
for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Nick Berry [aut],
Stephanie Reinders [aut, cre],
James Taylor [aut],
Felix Baez-Santiago [ctb],
Jon Gonzalez [...truncated...]
Maintainer: Stephanie Reinders <srein@iastate.edu>
Diff between handwriter versions 2.0.3 dated 2023-12-08 and 3.0.0 dated 2024-03-08
handwriter-2.0.3/handwriter/data/example_analysis_2chains.rda |only handwriter-2.0.3/handwriter/data/example_model_2chains.rda |only handwriter-2.0.3/handwriter/data/model_wrapped_cauchy.rda |only handwriter-2.0.3/handwriter/man/example_analysis_2chains.Rd |only handwriter-2.0.3/handwriter/man/example_model_2chains.Rd |only handwriter-2.0.3/handwriter/man/model_wrapped_cauchy.Rd |only handwriter-3.0.0/handwriter/DESCRIPTION | 13 handwriter-3.0.0/handwriter/MD5 | 57 - handwriter-3.0.0/handwriter/NAMESPACE | 2 handwriter-3.0.0/handwriter/NEWS.md | 11 handwriter-3.0.0/handwriter/R/BatchProcessing.R | 155 ++- handwriter-3.0.0/handwriter/R/ClusterMakeTemplates.R | 8 handwriter-3.0.0/handwriter/R/ClusterModeling_analysisfunctions.R | 5 handwriter-3.0.0/handwriter/R/ClusterModeling_clusterassignment.R | 485 +++++++--- handwriter-3.0.0/handwriter/R/ClusterModeling_datafunctions.R | 72 - handwriter-3.0.0/handwriter/R/ClusterModeling_modelfunctions.R | 12 handwriter-3.0.0/handwriter/R/ClusterModeling_plottingfunctions.R | 4 handwriter-3.0.0/handwriter/R/JunctionDetection.R | 351 ++++--- handwriter-3.0.0/handwriter/R/PlotFunctions.R | 3 handwriter-3.0.0/handwriter/R/data.R | 78 - handwriter-3.0.0/handwriter/README.md | 6 handwriter-3.0.0/handwriter/man/about_variable.Rd | 4 handwriter-3.0.0/handwriter/man/calculate_accuracy.Rd | 3 handwriter-3.0.0/handwriter/man/drop_burnin.Rd | 3 handwriter-3.0.0/handwriter/man/get_cluster_fill_counts.Rd |only handwriter-3.0.0/handwriter/man/get_clusters_batch.Rd |only handwriter-3.0.0/handwriter/man/handwriter-package.Rd | 2 handwriter-3.0.0/handwriter/man/plot_posterior_probabilities.Rd | 1 handwriter-3.0.0/handwriter/man/plot_trace.Rd | 3 handwriter-3.0.0/handwriter/man/process_batch_dir.Rd | 14 handwriter-3.0.0/handwriter/man/process_batch_list.Rd | 24 handwriter-3.0.0/handwriter/tests/testthat/test-ClusterModeling_analysisfunctions.R | 33 handwriter-3.0.0/handwriter/tests/testthat/test-ClusterModeling_modelfunctions.R | 76 - handwriter-3.0.0/handwriter/tests/testthat/test-processBatch.R |only 34 files changed, 785 insertions(+), 640 deletions(-)
Title: Event History Analysis
Description: Parametric proportional hazards fitting with left truncation and
right censoring for common families of distributions, piecewise constant
hazards, and discrete models. Parametric accelerated failure time models
for left truncated and right censored data. Proportional hazards
models for tabular and register data. Sampling of risk sets in Cox
regression, selections in the Lexis diagram, bootstrapping.
Broström (2022) <doi:10.1201/9780429503764>.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between eha versions 2.11.2 dated 2023-11-28 and 2.11.4 dated 2024-03-08
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + R/aftreg.R | 8 ++++---- R/logLik.R | 9 +++++++++ R/ltx2.R | 5 +---- R/toTpch.R | 5 +++-- inst/doc/eha.html | 4 ++-- inst/doc/gompertz.html | 4 ++-- inst/doc/parametric.html | 4 ++-- inst/doc/parametric1.pdf |binary inst/doc/tpchreg.html | 4 ++-- man/scania.Rd | 2 +- 14 files changed, 53 insertions(+), 37 deletions(-)
Title: Interactive Scatter Plot and Volcano Plot Labels
Description: Interactive labelling of scatter plots, volcano plots and
Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover
over points to see where specific points are located and click points
on/off to easily label them. Labels can be dragged around the plot to place
them optimally. Plots can be exported directly to PDF for publication.
Author: Myles Lewis [aut, cre] ,
Katriona Goldmann [aut] ,
Cankut Cubuk [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between easylabel versions 0.2.7 dated 2023-10-24 and 0.2.8 dated 2024-03-08
DESCRIPTION | 10 +- MD5 | 15 ++-- NAMESPACE | 1 NEWS.md | 8 ++ R/easyManhattan.R |only R/easyVolcano.R | 191 --------------------------------------------------- R/easylabel.R | 18 +++- build/vignette.rds |binary man/easyManhattan.Rd | 25 ++++-- 9 files changed, 52 insertions(+), 216 deletions(-)
Title: Plotting Tools for Anyone Working in Deep Time
Description: Extends the functionality of other plotting packages like
'ggplot2' and 'lattice' to help facilitate the plotting of data over long time
intervals, including, but not limited to, geological, evolutionary, and ecological
data. The primary goal of 'deeptime' is to enable users to add highly customizable
timescales to their visualizations. Other functions are also included to assist
with other areas of deep time visualization.
Author: William Gearty [aut, cre]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between deeptime versions 1.1.0 dated 2024-03-05 and 1.1.1 dated 2024-03-08
DESCRIPTION | 10 MD5 | 94 ++--- NAMESPACE | 2 NEWS.md | 7 R/coord_geo.R | 52 ++ R/coord_geo_polar.R | 44 ++ R/coord_geo_radial.R | 42 +- R/coord_trans_flip.R | 10 R/coord_trans_xy.R | 18 - R/deeptime-package.R | 15 R/facet_color.R | 45 +- R/get_scale_data.R | 20 - R/gggeo_scale.R | 3 R/gggeo_scale_old.R | 2 R/phylomorpho.R | 10 R/scales.R | 11 R/standalone-obj-type.R |only R/standalone-types-check.R |only inst/doc/coord_geo.R | 48 +- inst/doc/coord_geo.Rmd | 14 inst/doc/coord_geo.html | 8 inst/doc/phylogenies.html | 4 inst/doc/time.R | 3 inst/doc/time.Rmd | 3 inst/doc/time.html | 35 + man/coord_geo_polar.Rd | 10 man/coord_geo_radial.Rd | 7 man/gggeo_scale.Rd | 3 man/gggeo_scale_old.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/coord_geo_polar/coord-geo-polar-grey-new.svg |only tests/testthat/_snaps/coord_geo_polar/coord-geo-polar-new.svg | 71 +--- tests/testthat/_snaps/coord_geo_polar/coord-geo-polar-old.svg | 71 +--- tests/testthat/_snaps/coord_geo_polar/coord-geo-polar-pos-new.svg |only tests/testthat/_snaps/coord_geo_polar/stacked-scales-new.svg | 171 ++++----- tests/testthat/_snaps/coord_geo_polar/stacked-scales-old.svg | 171 ++++----- tests/testthat/_snaps/coord_geo_radial/stacked-scales-new.svg | 176 +++++----- tests/testthat/_snaps/coord_trans_flip/coord-trans-flip-with-different-transforms-old.svg |only tests/testthat/_snaps/coord_trans_xy/coord-trans-xy-with-no-trans-new.svg |only tests/testthat/setup-data.R | 6 tests/testthat/test-coord_geo.R | 33 + tests/testthat/test-coord_geo_polar.R | 75 ++-- tests/testthat/test-coord_geo_radial.R | 9 tests/testthat/test-coord_trans_xy.R | 18 + tests/testthat/test-get_scale_data.R | 1 tests/testthat/test-gggeo_scale_old.R | 1 vignettes/coord_geo-1.png |only vignettes/coord_geo-2.png |only vignettes/coord_geo.Rmd | 14 vignettes/phylogenies-1.png |binary vignettes/phylogenies-2.png |binary vignettes/time.Rmd | 3 52 files changed, 792 insertions(+), 550 deletions(-)
Title: Mapping Data for 'usmap' Package
Description: Provides a container for data used by the 'usmap' package.
The data used by 'usmap' has been extracted into this package so that the
file size of the 'usmap' package can be reduced greatly. The data in this
package will be updated roughly once per year as new map data files are
provided by the US Census Bureau.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <dilorenzo@hey.com>
Diff between usmapdata versions 0.2.1 dated 2024-02-04 and 0.2.2 dated 2024-03-08
DESCRIPTION | 10 MD5 | 32 +- NAMESPACE | 12 NEWS.md | 11 R/create-us-map.R | 514 ++++++++++++++++++++-------------------- R/fips-data.R | 54 ++-- R/us-map.R | 172 ++++++------- R/usmapdata-package.R | 102 +++---- README.md | 196 +++++++-------- man/centroid_labels.Rd | 46 +-- man/create_us_map.Rd | 148 +++++------ man/fips_data.Rd | 58 ++-- man/us_map.Rd | 98 +++---- man/usmapdata.Rd | 104 ++++---- tests/testthat.R | 24 - tests/testthat/test-fips-data.R | 82 +++--- tests/testthat/test-usmap.R | 152 +++++------ 17 files changed, 914 insertions(+), 901 deletions(-)
Title: Spacekime Analytics, Time Complexity and Inferential Uncertainty
Description: Provide the core functionality to transform longitudinal data to
complex-time (kime) data using analytic and numerical techniques, visualize the original
time-series and reconstructed kime-surfaces, perform model based (e.g., tensor-linear regression)
and model-free classification and clustering methods in the book Dinov, ID and Velev, MV. (2021)
"Data Science: Time Complexity, Inferential Uncertainty, and Spacekime Analytics", De Gruyter STEM Series,
ISBN 978-3-11-069780-3. <https://www.degruyter.com/view/title/576646>.
The package includes 18 core functions which can be separated into three groups.
1) draw longitudinal data, such as Functional magnetic resonance imaging(fMRI) time-series, and forecast or transform the time-series data.
2) simulate real-valued time-series data, e.g., fMRI time-courses, detect the activated areas,
report the corresponding p-values, and visualize the p-values in the 3D brain space.
3) Laplace transform and kimesurface reconstructions of the fMRI d [...truncated...]
Author: Yongkai Qiu [aut, cre],
Zhe Yin [aut],
Jinwen Cao [aut],
Yupeng Zhang [aut],
Yuyao Liu [aut],
Rongqian Zhang [aut],
Rouben Rostamian [ctb],
Ranjan Maitra [ctb],
Daniel Rowe [ctb],
Daniel Adrian [ctb] ,
Yunjie Guo [aut],
Ivo Dinov [aut]
Maintainer: Yongkai Qiu <yongkai@umich.edu>
Diff between TCIU versions 1.2.4 dated 2023-10-06 and 1.2.5 dated 2024-03-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- data/sample_save.RData |binary inst/doc/tciu-LT-kimesurface.html | 20 ++++++++++---------- inst/doc/tciu-fMRI-analytics.html | 32 ++++++++++++++++---------------- 5 files changed, 33 insertions(+), 33 deletions(-)
Title: Bayesian Joint Latent Class and Regression Models
Description: For fitting Bayesian joint latent class and regression models using
Gibbs sampling. See the documentation for the model.
The technical details of the model implemented here are described in Elliott,
Michael R., Zhao, Zhangchen, Mukherjee, Bhramar, Kanaya, Alka, Needham,
Belinda L., "Methods to account for uncertainty in latent class assignments when
using latent classes as predictors in regression models, with application to
acculturation strategy measures" (2020) In press at Epidemiology
<doi:10.1097/EDE.0000000000001139>.
Author: Michael Elliot [aut],
Zhangchen Zhao [aut],
Michael Kleinsasser [aut, cre]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Diff between lcra versions 1.1.2 dated 2020-08-07 and 1.1.5 dated 2024-03-08
DESCRIPTION | 12 MD5 | 26 - NAMESPACE | 22 R/WinBUGS.R | 654 ++++++++++++++--------------- R/data.R | 276 ++++++------ R/lcra.R | 1072 ++++++++++++++++++++++++------------------------ R/write_model.R | 70 +-- README.md | 558 ++++++++++++------------ man/express.Rd | 60 +- man/latent3.Rd | 78 +-- man/latent3_binary.Rd | 78 +-- man/lcra.Rd | 612 +++++++++++++-------------- man/paper_sim.Rd | 70 +-- man/paper_sim_binary.Rd | 70 +-- 14 files changed, 1825 insertions(+), 1833 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-04 1.1.1
2023-08-25 1.1.0
2023-04-27 1.0.3
2022-03-10 1.0.2
2022-03-07 1.0.1
Title: K's "Don't Repeat Yourself"-Collection
Description: A collection of personal helper functions to avoid redundancy
in the spirit of the "Don't repeat yourself" principle of software
development (<https://en.wikipedia.org/wiki/Don%27t_repeat_yourself>).
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between kdry versions 0.0.1 dated 2023-04-18 and 0.0.2 dated 2024-03-08
DESCRIPTION | 15 - MD5 | 100 +++--- NAMESPACE | 51 +-- R/base_icolnames.R | 44 +- R/base_list_append.R | 64 ++-- R/base_list_update.R | 70 ++-- R/dtr_matrix2df.R | 84 ++--- R/misc_argument_catcher.R | 84 ++--- R/misc_duplicated_by_names.R | 50 +-- R/misc_recursive_copy.R | 136 ++++----- R/misc_subset_options.R | 58 +-- R/mlh_outsample_row_indices.R | 190 ++++++------ R/mlh_reshape.R | 74 ++-- R/mlh_subset.R | 156 +++++----- R/pch_check_available_cores.R | 82 ++--- R/pch_clean_up.R | 54 +-- R/pch_register_parallel.R | 52 +-- R/plt_parallel_coordinates.R | 582 +++++++++++++++++++-------------------- R/rep_distribution_utils.R | 62 ++-- R/rep_frac_pct.R |only R/rep_mean_sd.R | 158 +++++----- R/rep_median_ci.R | 222 +++++++------- R/rep_pval.R | 104 +++--- R/rep_sum_pct.R | 110 +++---- R/sts_normalize.R | 54 +-- R/zzz.R | 6 man/dtr_matrix2df.Rd | 60 ++-- man/list.append.Rd | 68 ++-- man/list.update.Rd | 70 ++-- man/misc_argument_catcher.Rd | 60 ++-- man/misc_duplicated_by_names.Rd | 54 +-- man/misc_recursive_copy.Rd | 70 ++-- man/misc_subset_options.Rd | 52 +-- man/mlh_outsample_row_indices.Rd | 84 ++--- man/mlh_subset.Rd | 54 +-- man/pch_check_available_cores.Rd | 50 +-- man/pch_clean_up.Rd | 56 +-- man/pch_register_parallel.Rd | 58 +-- man/plt_parallel_coordinates.Rd | 126 ++++---- man/rep_frac_pct.Rd |only man/rep_mean_sd.Rd | 116 +++---- man/rep_median_ci.Rd | 128 ++++---- man/sts_normalize.Rd | 50 +-- tests/testthat/_snaps/rep.md | 4 tests/testthat/test-base_lists.R | 128 ++++---- tests/testthat/test-dtr.R | 40 +- tests/testthat/test-lints.R | 26 - tests/testthat/test-misc.R | 158 +++++----- tests/testthat/test-pch.R | 40 +- tests/testthat/test-plt.R | 18 - tests/testthat/test-rep.R | 160 +++++----- tests/testthat/test-sts.R | 42 +- 52 files changed, 2229 insertions(+), 2205 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation using a single or multiple Markov chains. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al., 1991, <doi:10.1007/BF00116466>) and Leroux model (Leroux et al., 2000, <doi:10.1007/978-1-4612-1284-3_4>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within are [...truncated...]
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 6.1 dated 2023-11-17 and 6.1.1 dated 2024-03-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/binomial.RAB.R | 42 +++++++++++------------------------------- R/gaussian.RAB.R | 37 ++++++++++--------------------------- R/poisson.RAB.R | 44 +++++++++++--------------------------------- build/vignette.rds |binary inst/doc/CARBayes.Rnw | 6 +++--- inst/doc/CARBayes.pdf |binary man/CARBayes-package.Rd | 8 ++++++-- man/S.RAB.Rd | 10 ++++------ vignettes/CARBayes.Rnw | 6 +++--- 11 files changed, 62 insertions(+), 119 deletions(-)
Title: R6-Based ML Survival Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners for survival analysis. The package
provides R6-based survival learners for the following algorithms:
'glmnet' <https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'rpart'
<https://CRAN.R-project.org/package=rpart>. These can be used directly
with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlsurvlrnrs versions 0.0.2 dated 2023-08-12 and 0.0.3 dated 2024-03-08
DESCRIPTION | 8 MD5 | 78 - NAMESPACE | 24 R/learner_surv_coxph_cox.R | 316 +++---- R/learner_surv_glmnet_cox.R | 526 ++++++------ R/learner_surv_xgboost_aft.R | 504 ++++++------ R/learner_surv_xgboost_cox.R | 332 ++++---- R/surv_c_index.R | 54 - R/zzz.R | 50 - build/vignette.rds |binary inst/doc/mlsurvlrnrs_glmnet_survival.R | 2 inst/doc/mlsurvlrnrs_glmnet_survival.Rmd | 1030 ++++++++++++------------- inst/doc/mlsurvlrnrs_ranger_survival.R | 2 inst/doc/mlsurvlrnrs_ranger_survival.Rmd | 914 +++++++++++----------- inst/doc/mlsurvlrnrs_rpart_survival.R | 2 inst/doc/mlsurvlrnrs_rpart_survival.Rmd | 876 ++++++++++----------- inst/doc/mlsurvlrnrs_xgboost_survival_aft.R | 2 inst/doc/mlsurvlrnrs_xgboost_survival_aft.Rmd | 928 +++++++++++----------- inst/doc/mlsurvlrnrs_xgboost_survival_cox.R | 2 inst/doc/mlsurvlrnrs_xgboost_survival_cox.Rmd | 908 +++++++++++----------- man/LearnerSurvCoxPHCox.Rd | 280 +++--- man/LearnerSurvGlmnetCox.Rd | 304 +++---- man/LearnerSurvRangerCox.Rd | 310 +++---- man/LearnerSurvRpartCox.Rd | 334 ++++---- man/LearnerSurvXgboostAft.Rd | 352 ++++---- man/LearnerSurvXgboostCox.Rd | 344 ++++---- man/c_index.Rd | 66 - tests/testthat.R | 24 tests/testthat/test-lints.R | 26 tests/testthat/test-surv_coxph_cox.R | 128 +-- tests/testthat/test-surv_glmnet_cox.R | 214 ++--- tests/testthat/test-surv_ranger_cox.R | 236 ++--- tests/testthat/test-surv_rpart_cox.R | 230 ++--- tests/testthat/test-surv_xgboost_aft.R | 248 +++--- tests/testthat/test-surv_xgboost_cox.R | 246 ++--- vignettes/mlsurvlrnrs_glmnet_survival.Rmd | 1030 ++++++++++++------------- vignettes/mlsurvlrnrs_ranger_survival.Rmd | 914 +++++++++++----------- vignettes/mlsurvlrnrs_rpart_survival.Rmd | 876 ++++++++++----------- vignettes/mlsurvlrnrs_xgboost_survival_aft.Rmd | 928 +++++++++++----------- vignettes/mlsurvlrnrs_xgboost_survival_cox.Rmd | 908 +++++++++++----------- 40 files changed, 7278 insertions(+), 7278 deletions(-)
Title: Basic Functions to Check Readability, Consistency, and Content
of an Individual Participant Data File
Description: Basic checks needed with an individual level participant data from randomised controlled trial. This
checks files for existence, read access and individual columns for formats. The checks on format is currently implemented for gender and age formats.
Author: Sheeja Manchira Krishnan
Maintainer: Sheeja Manchira Krishnan <sheejamk@gmail.com>
Diff between IPDFileCheck versions 0.7.5 dated 2022-02-01 and 0.8.1 dated 2024-03-08
IPDFileCheck-0.7.5/IPDFileCheck/R/IPDFileCheck.R |only IPDFileCheck-0.8.1/IPDFileCheck/DESCRIPTION | 11 IPDFileCheck-0.8.1/IPDFileCheck/MD5 | 90 - IPDFileCheck-0.8.1/IPDFileCheck/NAMESPACE | 89 - IPDFileCheck-0.8.1/IPDFileCheck/R/IPDFilecheck.R |only IPDFileCheck-0.8.1/IPDFileCheck/build/vignette.rds |binary IPDFileCheck-0.8.1/IPDFileCheck/inst/doc/User_Guide.R | 2 IPDFileCheck-0.8.1/IPDFileCheck/inst/doc/User_Guide.html | 672 +++++++--- IPDFileCheck-0.8.1/IPDFileCheck/man/calculate_age_from_dob.Rd | 78 - IPDFileCheck-0.8.1/IPDFileCheck/man/calculate_age_from_year.Rd | 58 IPDFileCheck-0.8.1/IPDFileCheck/man/check_col_pattern_colname.Rd | 52 IPDFileCheck-0.8.1/IPDFileCheck/man/check_column_exists.Rd | 46 IPDFileCheck-0.8.1/IPDFileCheck/man/check_load_packages.Rd | 40 IPDFileCheck-0.8.1/IPDFileCheck/man/cohensd.Rd | 44 IPDFileCheck-0.8.1/IPDFileCheck/man/convert_date_numeric_stdform.Rd | 52 IPDFileCheck-0.8.1/IPDFileCheck/man/convert_date_string_stdform.Rd | 46 IPDFileCheck-0.8.1/IPDFileCheck/man/convert_to_number.Rd | 40 IPDFileCheck-0.8.1/IPDFileCheck/man/descriptive_stats_col_excl_nrcode.Rd | 54 IPDFileCheck-0.8.1/IPDFileCheck/man/get_colno_pattern_colname.Rd | 48 IPDFileCheck-0.8.1/IPDFileCheck/man/get_columnno_fornames.Rd | 46 IPDFileCheck-0.8.1/IPDFileCheck/man/get_contents_cols.Rd | 50 IPDFileCheck-0.8.1/IPDFileCheck/man/get_effect_size.Rd | 46 IPDFileCheck-0.8.1/IPDFileCheck/man/get_mode_from_vector.Rd | 44 IPDFileCheck-0.8.1/IPDFileCheck/man/get_sem.Rd | 44 IPDFileCheck-0.8.1/IPDFileCheck/man/get_summary_gtsummary.Rd | 70 - IPDFileCheck-0.8.1/IPDFileCheck/man/get_value_from_codes.Rd | 60 IPDFileCheck-0.8.1/IPDFileCheck/man/keep_required_columns.Rd | 52 IPDFileCheck-0.8.1/IPDFileCheck/man/present_mean_sd_rmna_text.Rd | 58 IPDFileCheck-0.8.1/IPDFileCheck/man/represent_categorical_data_exclude_missing.Rd | 52 IPDFileCheck-0.8.1/IPDFileCheck/man/represent_categorical_data_forsubgroups.Rd | 68 - IPDFileCheck-0.8.1/IPDFileCheck/man/represent_categorical_data_include_missing.Rd | 52 IPDFileCheck-0.8.1/IPDFileCheck/man/represent_categorical_textdata.Rd | 52 IPDFileCheck-0.8.1/IPDFileCheck/man/represent_numerical_data_forsubgroups.Rd | 62 IPDFileCheck-0.8.1/IPDFileCheck/man/return_longitudinal_summary.Rd | 58 IPDFileCheck-0.8.1/IPDFileCheck/man/return_subgroup_omitna.Rd | 80 - IPDFileCheck-0.8.1/IPDFileCheck/man/return_subgroup_withNA.Rd | 58 IPDFileCheck-0.8.1/IPDFileCheck/man/test_age.Rd | 50 IPDFileCheck-0.8.1/IPDFileCheck/man/test_column_contents.Rd | 58 IPDFileCheck-0.8.1/IPDFileCheck/man/test_columnnames.Rd | 50 IPDFileCheck-0.8.1/IPDFileCheck/man/test_data_numeric.Rd | 62 IPDFileCheck-0.8.1/IPDFileCheck/man/test_data_numeric_norange.Rd | 58 IPDFileCheck-0.8.1/IPDFileCheck/man/test_data_string.Rd | 50 IPDFileCheck-0.8.1/IPDFileCheck/man/test_data_string_restriction.Rd | 64 IPDFileCheck-0.8.1/IPDFileCheck/man/test_file_exist_read.Rd | 44 IPDFileCheck-0.8.1/IPDFileCheck/man/test_gender.Rd | 54 IPDFileCheck-0.8.1/IPDFileCheck/tests/testthat.R | 8 IPDFileCheck-0.8.1/IPDFileCheck/tests/testthat/test-IPDFilecheck.R | 4 47 files changed, 1602 insertions(+), 1274 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.1.1 dated 2024-02-28 and 1.2.0 dated 2024-03-08
DESCRIPTION | 10 MD5 | 36 - NAMESPACE | 3 NEWS.md | 8 R/boundaries.R |only R/utils-general.R | 29 inst/doc/grates.R | 47 - inst/doc/grates.Rmd | 92 +- inst/doc/grates.html | 1321 ++++++++++++++++---------------------- man/boundaries.Rd |only tests/testthat/test-epiweek.R | 9 tests/testthat/test-isoweek.R | 9 tests/testthat/test-month.R | 10 tests/testthat/test-period.R | 8 tests/testthat/test-plots.R | 77 -- tests/testthat/test-year.R | 10 tests/testthat/test-yearmonth.R | 10 tests/testthat/test-yearquarter.R | 10 tests/testthat/test-yearweek.R | 28 vignettes/grates.Rmd | 92 +- 20 files changed, 923 insertions(+), 886 deletions(-)
Title: Fast Estimation of CUB Models via Louis' Identity
Description: For ordinal rating data, consider the accelerated EM algorithm to estimate and test models within the family of
CUB models (where CUB stands for Combination of a
discrete Uniform and a shifted Binomial distributions). The procedure is built upon Louis' identity for the observed information matrix. Best-subset variable selection is then implemented since it becomes more feasible from the computational point of view.
Author: Rosaria Simone [aut, cre]
Maintainer: Rosaria Simone <rosaria.simone@unina.it>
Diff between FastCUB versions 0.0.2 dated 2020-02-12 and 0.0.3 dated 2024-03-08
DESCRIPTION | 22 +- MD5 | 132 ++++++++-------- NAMESPACE | 59 +++---- R/bestcub.R | 324 +++++++++++------------------------------ R/decomp.R | 96 ++++++++---- R/dissim.R | 5 R/fastCUB.R | 292 +++++++++++++++---------------------- R/fastCUB_package.R | 11 - R/fastcub00.R | 64 +++----- R/fastcub0q.R | 137 +++++------------ R/fastcubp0.R | 137 +++++------------ R/fastcubpq.R | 151 +++++++++---------- R/fitted.R | 31 ++- R/inibestgama.R | 13 - R/invmatgen.R | 4 R/kkk.R | 2 R/loglikcub00.R | 14 - R/loglikcub0q.R | 48 +++--- R/loglikcubp0.R | 55 +++---- R/makeplot.R | 16 +- R/parnames.R | 101 ++++++------ R/print.R | 10 - R/probcubpq.R | 28 +-- R/relgoods.R | 1 R/summary.R | 381 +++++++++++++++++++++++-------------------------- R/univer.R | 1 R/vcov.R | 28 +-- man/BIC.fastCUB.Rd | 46 ++--- man/Hadprod.Rd | 56 +++---- man/bestcub.Rd | 128 ++++++---------- man/bitcsi.Rd | 74 ++++----- man/bitgama.Rd | 78 +++++----- man/coef.fastCUB.Rd | 52 +++--- man/cormat.Rd | 48 +++--- man/decomp.Rd | 66 ++++---- man/dissim.Rd | 52 +++--- man/effe01.Rd | 48 +++--- man/effe10.Rd | 50 +++--- man/fastCUB.Rd | 100 ++++-------- man/fastCUB_package.Rd | 57 +++---- man/fastcub00.Rd | 68 ++++---- man/fastcub0q.Rd | 68 ++++---- man/fastcubp0.Rd | 68 ++++---- man/fastcubpq.Rd | 78 ++++------ man/fitted.fastCUB.Rd | 48 +++--- man/inibest.Rd | 78 +++++----- man/inibestgama.Rd | 84 +++++----- man/invmatgen.Rd | 58 +++---- man/kkk.Rd | 38 ++-- man/logLik.fastCUB.Rd | 46 ++--- man/logis.Rd | 56 +++---- man/loglikcub00.Rd | 44 ++--- man/loglikcub0q.Rd | 50 +++--- man/loglikcubp0.Rd | 50 +++--- man/loglikcubpq.Rd | 56 +++---- man/makeplot.Rd | 48 +++--- man/parnames.Rd | 43 ++--- man/print.fastCUB.Rd | 42 ++--- man/probbit.Rd | 60 +++---- man/probcub00.Rd | 74 ++++----- man/probcub0q.Rd | 110 +++++++------- man/probcubp0.Rd | 106 ++++++------- man/probcubpq.Rd | 112 +++++++------- man/relgoods.Rd | 211 +++++++++++++-------------- man/summary.fastCUB.Rd | 53 +++--- man/univer.Rd | 99 ++++++------ man/vcov.fastCUB.Rd | 49 +++--- 67 files changed, 2284 insertions(+), 2631 deletions(-)
Title: Recording Synchronisation, Call Detection and Assignment, Audio
Analysis
Description: Intended to analyse recordings from multiple microphones (e.g., backpack
microphones in captive setting). It allows users to align recordings even if there is non-linear
drift of several minutes between them. A call detection and assignment pipeline can be used
to find vocalisations and assign them to the vocalising individuals (even if the vocalisation
is picked up on multiple microphones). The tracing and measurement functions allow for detailed
analysis of the vocalisations and filtering of noise. Finally, the package includes a function
to run spectrographic cross correlation, which can be used to compare vocalisations. It also
includes multiple other functions related to analysis of vocal behaviour.
Author: Simeon Q. Smeele [cre, aut],
Stephen A. Tyndel [ctb]
Maintainer: Simeon Q. Smeele <simeonqs@hotmail.com>
Diff between callsync versions 0.0.6 dated 2023-02-15 and 0.2.1 dated 2024-03-08
DESCRIPTION | 9 - MD5 | 105 ++++++++++--------- NAMESPACE | 3 NEWS.md | 25 ++++ R/align.R | 45 ++++++-- R/better.spectro.R | 18 +++ R/calc.am.R | 14 ++ R/calc.fm.R | 27 ++++ R/calc.perf.R | 99 +++++++++++++++--- R/call.assign.R | 35 ++++++ R/call.detect.R | 44 +++++--- R/call.detect.multiple.R | 136 ++++++++++++++++++++----- R/create.spec.object.R | 38 +++++- R/detect.and.assign.R | 79 ++++++++++---- R/export.detections.R |only R/load.selection.table.R |only R/load.selection.tables.R | 38 ++---- R/load.selection.tables.audacity.R | 17 ++- R/load.wave.R | 13 ++ R/measure.trace.R | 22 +++- R/measure.trace.multiple.R | 75 ++++++++++--- R/run.spcc.R | 57 ++++++++-- R/simple.cc.R | 12 +- R/sliding.pixel.comparison.R | 32 +++++ R/trace.fund.R | 46 ++++++-- build |only inst/doc |only man/align.Rd | 29 +++++ man/better.spectro.Rd | 16 ++ man/calc.am.Rd | 15 ++ man/calc.fm.Rd | 23 +++- man/calc.perf.Rd | 34 ++++-- man/call.assign.Rd | 35 ++++++ man/call.detect.Rd | 42 +++++-- man/call.detect.multiple.Rd | 75 ++++++++++--- man/callsync.Rd |only man/create.spec.object.Rd | 39 +++++-- man/detect.and.assign.Rd | 69 +++++++++--- man/export.detections.Rd |only man/load.selection.table.Rd |only man/load.selection.tables.Rd | 9 + man/load.selection.tables.audacity.Rd | 18 +++ man/load.wave.Rd | 14 ++ man/measure.trace.Rd | 23 +++- man/measure.trace.multiple.Rd | 45 ++++++-- man/run.spcc.Rd | 52 +++++++-- man/simple.cc.Rd | 11 +- man/sliding.pixel.comparison.Rd | 33 +++++- man/trace.fund.Rd | 41 ++++++- tests/testthat/Rplots.pdf |binary tests/testthat/files/chunk@1@1@1@1.wav |binary tests/testthat/files/chunk@2@1@1@1.wav |binary tests/testthat/test_align.R | 67 +++++++----- tests/testthat/test_call.assign.R | 54 ++++----- tests/testthat/test_create.spec.object.R |only tests/testthat/test_export.detections.R |only tests/testthat/test_sliding.pixel.comparison.R |only vignettes |only 58 files changed, 1352 insertions(+), 381 deletions(-)
Title: PKPD, PBPK, and Systems Pharmacology Modeling Tools
Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between ubiquity versions 2.0.1 dated 2023-10-29 and 2.0.3 dated 2024-03-08
ubiquity-2.0.1/ubiquity/inst/doc/NCA.R |only ubiquity-2.0.1/ubiquity/inst/doc/NCA.Rmd |only ubiquity-2.0.1/ubiquity/inst/doc/NCA.html |only ubiquity-2.0.1/ubiquity/vignettes/NCA.Rmd |only ubiquity-2.0.1/ubiquity/vignettes/NCA_presim.RData |only ubiquity-2.0.3/ubiquity/DESCRIPTION | 8 ubiquity-2.0.3/ubiquity/MD5 | 45 -- ubiquity-2.0.3/ubiquity/NEWS.md | 272 +++++++------ ubiquity-2.0.3/ubiquity/R/ubiquity.r | 17 ubiquity-2.0.3/ubiquity/build/vignette.rds |binary ubiquity-2.0.3/ubiquity/inst/doc/Deployment.R | 32 - ubiquity-2.0.3/ubiquity/inst/doc/Deployment.html | 4 ubiquity-2.0.3/ubiquity/inst/doc/Estimation.Rmd | 2 ubiquity-2.0.3/ubiquity/inst/doc/Estimation.html | 2 ubiquity-2.0.3/ubiquity/inst/doc/Language.Rmd | 74 +++ ubiquity-2.0.3/ubiquity/inst/doc/Language.html | 73 +++ ubiquity-2.0.3/ubiquity/inst/doc/Reporting.html | 10 ubiquity-2.0.3/ubiquity/inst/doc/Simulation.R | 2 ubiquity-2.0.3/ubiquity/inst/doc/Simulation.html | 8 ubiquity-2.0.3/ubiquity/inst/doc/Titration.html | 12 ubiquity-2.0.3/ubiquity/inst/ubinc/perl/build_system.pl | 7 ubiquity-2.0.3/ubiquity/inst/ubinc/scripts/ubiquity_fcns.R | 17 ubiquity-2.0.3/ubiquity/man/system_fetch_nca.Rd | 2 ubiquity-2.0.3/ubiquity/vignettes/Estimation.Rmd | 2 ubiquity-2.0.3/ubiquity/vignettes/Language.Rmd | 74 +++ ubiquity-2.0.3/ubiquity/vignettes/Reporting.RData |binary 26 files changed, 459 insertions(+), 204 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2020) <arXiv:2004.11408> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>. 'cmdstanr' can be downloaded at <https://mc-stan.org/cmdstanr/>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.7.1 dated 2024-03-01 and 0.7.2 dated 2024-03-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/griddata_class.R | 6 +++--- man/grid.Rd | 12 ++++++------ 4 files changed, 16 insertions(+), 16 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between MiscMetabar versions 0.7.9 dated 2024-02-17 and 0.7.10 dated 2024-03-08
DESCRIPTION | 8 - MD5 | 56 ++++++------ NAMESPACE | 2 NEWS.md | 6 + R/beta_div_test.R | 2 R/dada_phyloseq.R | 8 - R/krona.R | 4 R/miscellanous.R | 45 +++++++++ R/plot_functions.R | 142 ++++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MiscMetabar.html | 101 ++++++++++++---------- man/SRS_curve_pq.Rd | 7 + man/build_phytree_pq.Rd | 2 man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/heat_tree_pq.Rd | 56 ++++++------ man/hill_pq.Rd | 5 + man/iNEXT_pq.Rd | 52 +++++------ man/is_krona_installed.Rd |only man/is_mumu_installed.Rd |only man/krona.Rd | 2 man/lulu_pq.Rd | 2 man/merge_krona.Rd | 2 man/mumu_pq.Rd | 2 man/plot_LCBD_pq.Rd | 2 man/plot_guild_pq.Rd | 2 man/rotl_pq.Rd | 10 +- tests/testthat/Rplots.pdf |binary vignettes/bibliography.bib | 16 +++ 30 files changed, 323 insertions(+), 211 deletions(-)
Title: 'Shiny' Application for R Package 'fitODBOD'
Description: For binomial outcome data Alternate Binomial Distributions
and Binomial Mixture Distributions are fitted when overdispersion is
available.
Author: Amalan Mahendran [cre, aut]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBODRshiny versions 1.0.1 dated 2024-02-26 and 1.0.2 dated 2024-03-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- data/All_Plots.rda |binary 3 files changed, 6 insertions(+), 6 deletions(-)
More information about fitODBODRshiny at CRAN
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Title: A Fast and Flexible Bayesian Tool for Estimating Epidemiological
Parameters
Description: Estimation of epidemiological parameters with
Laplacian-P-splines following the methodology of Gressani et al. (2022)
<doi:10.1371/journal.pcbi.1010618>.
Author: Oswaldo Gressani [aut, cre] ,
Bryan Sumalinab [ctb]
Maintainer: Oswaldo Gressani <oswaldo_gressani@hotmail.fr>
Diff between EpiLPS versions 1.2.0 dated 2023-08-30 and 1.3.0 dated 2024-03-08
DESCRIPTION | 17 ++++++---- MD5 | 57 ++++++++++++++++++++++------------- NAMESPACE | 4 ++ NEWS.md | 10 ++++++ R/KerMCMC.R | 9 +++-- R/RcppExports.R | 4 ++ R/S3_Rt_plot.R | 9 +++-- R/S3_Rtnow_plot.R |only R/S3_nowcast_plot.R |only R/cov19incidence2022.R |only R/cov19mort2021.R |only R/estimR.R | 51 ++++++++++++++----------------- R/estimRmcmc.R | 61 +++++++++++++++++++++----------------- R/nowcasting.R |only R/nowcastingR.R |only R/perfRestim.R | 12 +++---- README.md | 34 +++++++++++++-------- build/vignette.rds |binary data/cov19incidence2022.rda |only data/cov19mort2021.rda |only inst/CITATION | 30 +++--------------- inst/COPYRIGHTS | 5 +-- inst/doc/Reproduction-number.R | 8 ++-- inst/doc/Reproduction-number.html | 36 +++++++++++----------- man/cov19incidence2022.Rd |only man/cov19mort2021.Rd |only man/estimR.Rd | 48 ++++++++++++++--------------- man/estimRmcmc.Rd | 56 ++++++++++++++++++---------------- man/nowcasting.Rd |only man/nowcastingR.Rd |only man/perfRestim.Rd | 12 +++---- man/plot.Rtnow.Rd |only man/plot.nowcasted.Rd |only src/KerLaplaceIncub.cpp | 8 ---- src/KerLaplaceNowcast.cpp |only src/KerRpostmap.cpp | 2 - src/RcppExports.cpp | 16 +++++++++ 37 files changed, 266 insertions(+), 223 deletions(-)
Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter.
Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between autostsm versions 3.1.3 dated 2024-02-08 and 3.1.4 dated 2024-03-08
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 6 + R/stsm_detect_breaks.R | 36 +++--- inst/doc/autostsm_vignette.R | 6 - inst/doc/autostsm_vignette.Rmd | 6 - inst/doc/autostsm_vignette.html | 230 +++++++++++++++++++--------------------- vignettes/autostsm_vignette.Rmd | 6 - 8 files changed, 147 insertions(+), 165 deletions(-)
Title: Kim Filter
Description: 'Rcpp' implementation of the multivariate Kim filter, which combines the Kalman and Hamilton filters for state probability inference.
The filter is designed for state space models and can handle missing values and exogenous data in the observation and state equations.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kimfilter versions 1.0.2 dated 2023-09-25 and 1.0.3 dated 2024-03-08
DESCRIPTION | 8 +- MD5 | 24 ++++--- NEWS.md | 6 + R/RcppExports.R | 95 +++++-------------------------- R/kim_filter.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/kimfilter_vignette.html | 4 - man/kim_filter.Rd | 24 ++++--- man/kim_filter_cpp.Rd |only man/ss_prob.Rd | 9 -- src/RcppExports.cpp | 14 ++-- src/kimfilter.cpp | 119 +++++++++++---------------------------- tests/testthat.R | 2 14 files changed, 101 insertions(+), 204 deletions(-)
Title: Analyze and Create Elegant Directed Acyclic Graphs
Description: Tidy, analyze, and plot directed acyclic graphs (DAGs).
'ggdag' is built on top of 'dagitty', an R package that uses the
'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing
DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using
'ggplot2' and 'ggraph', as well as common analytic and graphical
functions, such as determining adjustment sets and node relationships.
Author: Malcolm Barrett [aut, cre]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between ggdag versions 0.2.11 dated 2024-01-24 and 0.2.12 dated 2024-03-08
DESCRIPTION | 6 - MD5 | 38 ++++++------ NEWS.md | 3 build/vignette.rds |binary inst/doc/bias-structures.R | 7 +- inst/doc/bias-structures.Rmd | 7 +- inst/doc/bias-structures.html | 32 +++++----- inst/doc/intro-to-dags.R | 7 +- inst/doc/intro-to-dags.Rmd | 9 ++ inst/doc/intro-to-dags.html | 28 ++++---- inst/doc/intro-to-ggdag.R | 7 +- inst/doc/intro-to-ggdag.Rmd | 7 +- inst/doc/intro-to-ggdag.html | 128 ++++++++++++++++++++++++----------------- tests/testthat/helper-vdiffr.R | 1 tests/testthat/test-layouts.R | 2 tests/testthat/test-pull.R | 3 tests/testthat/test-tidy_dag.R | 2 vignettes/bias-structures.Rmd | 7 +- vignettes/intro-to-dags.Rmd | 9 ++ vignettes/intro-to-ggdag.Rmd | 7 +- 20 files changed, 194 insertions(+), 116 deletions(-)